Prerequisites

1. This pipeline is written in nextflow. Install nextflow by following the steps at Nextflow Installation Guide

2. The processes run on Docker containers. Install docker engine by following steps at Docker Installation Guide for Ubuntu

3. Pull the following docker images used in this pipeline:

docker pull staphb/pangolin:latest
docker pull nextstrain/nextclade:latest
docker pull ufuomababatunde/bammix:v1.0.0
docker pull staphb/freyja:latest
docker pull pegi3s/samtools_bcftools:latest
docker pull vandhanak/bcftools:1.3.1
docker pull rocker/r-rmd:latest

How to use CoPi

1. Download this github repository using git clone.

cd ~
git clone https://github.com/lanadelrea/CoPi

2. Navigate to the directory where CoPi is downloaded. Run the pipeline by indicating the path to the input and output folders. The input directory should contain fasta, fastq, bam, and bam index files.

cd ~
nextflow run CoPi --in_dir <input directory> --out_dir <output directory>

For example:

cd ~
nextflow run CoPi --in_dir /mnt/c/Samples --out_dir /mnt/c/Results

Results

Output directory will have 8 folders containing results from each step used to test for SARS-CoV-2 variant coinfection. The summary report is in the final folder named 08-Report.

Test the pipeline using sample files

To test the pipeline, use the files from CoPi Sample Files. Decompress samples.tar.xz by:

xz -d samples.tar.xz